Differential expression of small RNAs from smallRNAseq datasets

Question

[Aiswarya]

Hai,

I want to look at the differential expressions of small noncoding RNAs (specifically piRNAs) from small RNA-Seq datasets. I have found a few papers on those, but they are all slightly different in their methods. I was wondering if there is a standard pipeline suitable for this type of analysis. I would appreciate any advice.

Thanks in advance

[Marcel Ribeiro-Dantas]

I'm not sure about noncoding RNAs but maybe it could be a good start to have a look at this pipeline: https://nf-co.re/smrnaseq